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avoid contained hits due to split

This commit is contained in:
Heng Li 2017-06-25 11:43:50 -04:00
parent f20d550a59
commit 56364200c8
1 changed files with 14 additions and 8 deletions
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22
align.c
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@ -142,15 +142,21 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_adjust_minier(mi, qseq0, &a[r->as], &rs, &qs);
mm_adjust_minier(mi, qseq0, &a[r->as + r->cnt - 1], &re, &qe);
if (qs > 0 && rs > 0) { // actually this is always true
l = qs < opt->max_gap? qs : opt->max_gap;
qs0 = qs - l;
l += (l * opt->a - opt->q) / opt->e;
l = l < opt->max_gap? l : opt->max_gap;
l = l < rs? l : rs;
rs0 = rs - l;
} else rs0 = rs, qs0 = qs;
// compute rs0 and qs0
if (r->split && r->as > 0) {
mm_adjust_minier(mi, qseq0, &a[r->as-1], &rs0, &qs0);
} else {
if (qs > 0 && rs > 0) { // actually this is always true
l = qs < opt->max_gap? qs : opt->max_gap;
qs0 = qs - l;
l += (l * opt->a - opt->q) / opt->e;
l = l < opt->max_gap? l : opt->max_gap;
l = l < rs? l : rs;
rs0 = rs - l;
} else rs0 = rs, qs0 = qs;
}
// compute re0 and qe0
if (qe < qlen && re < mi->seq[rid].len) {
l = qlen - qe < opt->max_gap? qlen - qe : opt->max_gap;
qe0 = qe + l;